SMTL ID : 8uft.1 (1 other biounit)

Structure of human endothelial nitric oxide synthase P370N mutant heme domain in complex with 4-methyl-7-(4-methyl-2,3,4,5-tetrahydrobenzo[f][1,4]oxazepin-7-yl)quinolin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 19 residues within 4Å: Chain A: W.138, A.141, R.143, C.144, V.145, L.153, S.186, F.313, S.314, G.315, W.316, M.318, E.321, W.407, F.433, Y.435 Ligands: H4B.2, WK2.3, ACT.4 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:W.138, A:W.138, A:W.138, A:A.141, A:L.153, A:F.313, A:F.313, A:F.313, A:F.313, A:W.316, A:E.321, A:W.407, A:W.407, A:F.433, A:F.433 Hydrogen bonds: A:E.321, A:E.321, A:Y.435 Water bridges: A:R.325 Salt bridges: A:R.143 pi-Stacking: A:W.138 Metal complexes: A:C.144 HEM.13: 20 residues within 4Å: Chain B: W.138, A.141, R.143, C.144, V.145, G.146, L.153, S.186, F.313, S.314, G.315, W.316, M.318, E.321, W.407, F.433, Y.435 Ligands: H4B.14, WK2.15, ACT.16 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:W.138, B:W.138, B:W.138, B:A.141, B:R.143, B:V.145, B:L.153, B:F.313, B:F.313, B:F.313, B:F.313, B:W.316, B:E.321, B:W.407, B:F.433, B:F.433, B:F.433 Hydrogen bonds: B:E.321, B:E.321 Water bridges: B:R.325 Salt bridges: B:R.143 pi-Stacking: B:W.138 Metal complexes: B:C.144

2 x H4B: 5,6,7,8-TETRAHYDROBIOPTERIN(Non-covalent)

H4B.2: 12 residues within 4Å: Chain A: S.62, V.64, R.325, A.406, W.407 Chain B: W.405, F.420, H.421, Q.422, E.423 Ligands: HEM.1, WK2.3 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.325, A:R.325, A:A.406, A:W.407 pi-Stacking: A:W.407, A:W.407 pi-Cation interactions: A:W.407 Hydrophobic interactions: B:E.423 H4B.14: 12 residues within 4Å: Chain A: W.405, F.420, H.421, Q.422, E.423 Chain B: S.62, V.64, R.325, A.406, W.407 Ligands: HEM.13, WK2.15 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.325, B:R.325, B:A.406, B:W.407 Water bridges: B:S.62, B:W.407 pi-Stacking: B:W.407, B:W.407 pi-Cation interactions: B:W.407 Hydrophobic interactions: A:E.423

2 x WK2: (7M)-4-methyl-7-(4-methyl-2,3,4,5-tetrahydro-1,4-benzoxazepin-7-yl)quinolin-2-amine(Non-covalent)

WK2.3: 10 residues within 4Å: Chain A: P.294, V.296, F.313, W.316, Y.317, E.321, R.332, W.407 Ligands: HEM.1, H4B.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.294, A:V.296, A:W.407 Hydrogen bonds: A:E.321 WK2.15: 10 residues within 4Å: Chain B: P.294, V.296, F.313, W.316, Y.317, E.321, R.325, W.407 Ligands: HEM.13, H4B.14 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.294, B:V.296, B:F.313, B:W.407 Hydrogen bonds: B:E.321

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 6 residues within 4Å: Chain A: G.146, Q.149, W.316, V.378, S.386 Ligands: HEM.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.149 Hydrogen bonds: A:S.386, A:S.386 Water bridges: A:Q.149 ACT.12: 8 residues within 4Å: Chain A: D.356, V.360, I.412, S.413 Chain B: D.356, V.360, I.412, S.413 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.412 Hydrogen bonds: A:S.413 ACT.16: 6 residues within 4Å: Chain B: G.146, Q.149, W.316, V.378, S.386 Ligands: HEM.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.149 Hydrogen bonds: B:W.316, B:S.386 Water bridges: B:Q.149

3 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.5: 2 residues within 4Å: Chain A: E.337, T.347 6 PLIP interactions: 6 interactions with chain A Water bridges: A:E.337, A:E.337, A:T.347, A:W.354, A:W.354 Salt bridges: A:E.337 BTB.17: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: GD.21 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.279 Salt bridges: B:E.281 BTB.18: 3 residues within 4Å: Chain B: D.257, E.258, P.259 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.258 Water bridges: B:E.258 Salt bridges: B:E.258

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Chain A: G.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.197 GOL.7: 1 residues within 4Å: Chain A: D.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.344 Water bridges: A:D.344 GOL.19: 2 residues within 4Å: Chain B: E.337, D.338 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.337, B:E.337

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 3 residues within 4Å: Chain A: Q.207, Y.317, N.326 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: Q.207, R.210, Y.291, Y.317, N.326 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 4 residues within 4Å: Chain A: C.54, C.59 Chain B: C.54, C.59 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:C.54, A:C.59, B:C.54, B:C.59

3 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.10: 1 residues within 4Å: Chain A: E.127 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.127, H2O.2, H2O.3, H2O.8, H2O.8 CA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GD: GADOLINIUM ATOM(Non-covalent)

GD.21: 3 residues within 4Å: Chain B: T.279, E.281 Ligands: BTB.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.279, B:E.281, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Crystallographic and Computational Insights into Isoform-Selective Dynamics in Nitric Oxide Synthase. Biochemistry (2024)

Release Date

2024-03-13

Peptides

Nitric oxide synthase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide synthase 3

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